HHsearch alignment for GI: 254780705 and conserved domain: TIGR02141

>TIGR02141 modB_ABC molybdate ABC transporter, permease protein; InterPro: IPR011867 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry describes the permease protein, ModB, of the molybdate ABC transporter. This system has been characterised in Escherichia coli , Staphylococcus carnosus Rhodobacter capsulatus and Azotobacter vinlandii . Molybdate is chemically similar to sulphate, thiosulphate, and selenate. These related substrates, and sometimes molybdate itself, can be transported by the homologous sulphate receptor. Some apparent molybdenum transport operons include a permease related to this ModB, although less similar than some sulphate permease proteins and not included in this model.; GO: 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport, 0016021 integral to membrane.
Probab=99.97  E-value=7.2e-30  Score=209.07  Aligned_cols=197  Identities=26%  Similarity=0.303  Sum_probs=161.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HCCC-C-C
Q ss_conf             99999999999999999999999864373024567898998876533699999999999986----------2666-3-0
Q gi|254780705|r  210 SLYMMLIVIGLSFPLGIASAIYLEEFSHKGFFSSFVQANINNLASVPSIVYGILGSAVLINF----------FKMP-R-S  277 (425)
Q Consensus       210 Tl~~~~ia~~ia~pigv~~aiyl~e~a~~~~~~~~i~~~i~~la~vPSIv~Gl~gl~~~~~~----------~~~~-~-~  277 (425)
T Consensus         3 Slk~A~~~Tl~~~~LGi~~A~~La~~--~f~gK~~le~L~~LPLVLPPtV~Gf~LL~~fG~~~G~~G~l~~~~~~~Gl~F   80 (212)
T TIGR02141         3 SLKVAVIATLLLLPLGIPVAWLLARS--RFRGKSLLEALVTLPLVLPPTVLGFYLLLAFGRNSGPIGKLLELLGISGLVF   80 (212)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHH
T ss_conf             99999999999999999999999886--1760454464443266356378999999988035740778988650685246


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04689753345436689999999985110678989987077212777788397533258999999999987677999998
Q gi|254780705|r  278 TALVGGLILALMTLPSIIIATGVALRTVPSSIRSAALGLGASKVQTVFHHVLPLAMPAILTGSTVSLARALGETAPLLFV  357 (425)
Q Consensus       278 ~~l~g~~~l~~m~lP~i~~~~~~al~~vp~~~~eaa~~LGas~~~~~~~v~lp~a~pgi~~g~il~~~ra~GEta~ll~~  357 (425)
T Consensus        81 t~~g~vlAs~~VSfPl~v~~~~~a~~~~~~~~~~~ArtLGaS~~~~f~~v~LPL~~pG~l~G~vL~FAR~LGEFGAtlm~  160 (212)
T TIGR02141        81 TFAGAVLASVVVSFPLMVRTIRGAFEAVDPDLEEAARTLGASELRVFLKVTLPLAFPGLLAGAVLSFARALGEFGATLMF  160 (212)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             69999999999997768999999998627128999988278789989999857328999999999999750211344310


Q ss_pred             HHHHHCCCCCCCCCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             543210136656134455799999986036-650069999999999999999999999999997
Q gi|254780705|r  358 GMVAFVTDYPVGVTDIATAFPVQIYLWAAD-AERPFVERTFGAILLLLIFLAVINTAMLWLRNR  420 (425)
Q Consensus       358 ~~~~~~~~~p~~~~~p~~tlp~~Iy~~~~~-~~~~~~~~~~aa~lvLl~~~~~~n~~a~~lr~r  420 (425)
T Consensus       161 aGN-----IpG----kT~T~plaIY~~v~~lg~---~~~A~~l~l~ll~~s~~~ll~~~~~~~R  212 (212)
T TIGR02141       161 AGN-----IPG----KTRTIPLAIYDAVESLGD---YEAAHLLSLVLLALSLIVLLLVELLNKR  212 (212)
T ss_pred             CCC-----CCC----CCHHHHHHHHHHHHCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             046-----979----630176778867705788---6789999999999999999999875059